Posted
by
Roblimo
on Tuesday November 20, 2012 @03:04PM
from the Igor-is-on-his-break-can-I-help-you? dept.

Imagine that you are at 33 Flatbush Ave. in the Brooklyn borough of what David Letterman calls "the world's greatest city." You go to the 7th floor. Congratulations. You have found New York City's community biolab, Genspace. It's a well-equipped facility without a single mad scientist in sight. Indeed, everyone here seems as happy as the people you see in a makerspace -- which should not be surprising, since Genspace is essentially a makerspace for biologists. It is confined to non-hazardous experiments, but there is plenty going on, including ongoing projects and courses with titles like DIY Neuroscience: Controlling Behavior from the Inside. You can keep up with Genspace by following their blog. And of course, if you're in the neighborhood you should stop in. It's a welcoming environment, dedicated to the idea that science is for everyone, not just a chosen few.

Oliver Medvedik: Hi. I’m Oliver. I’m a co-founder of Genspace. I have a Ph.D. in Molecular Biology and welcome to our community biotech lab. So, you’re standing in the middle of Genspace right now. So, let me give you a tour of this space.

So, right over here is Dr. Ellen Jorgensen, another co-founder, working on Genspace related projects. Here we have our teaching and office area where we essentially give classes in biotech. And over here in this glass cube is one of our BSL1 (Biosafety Level One) laboratories. So, here’s another laboratory behind this wall, so this is another BSL1 lab where we do lot of prep work. We also have incubators in here. And here is another laboratory zone that we are expanding into.

So, we have a fairly sizable area to do a variety of projects. So when people come to Genspace, they can either work on a project of their own devicing, so we offer a space for people to work on their projects or they can volunteer and work on somebody else’s project. Or, they can take a class and learn about biotech, so we offer a number of courses in genotyping, in biotechnology, in synthetic biology where they can learn hands-on the tools of the trade.

Timothy Lord: Can you talk a little bit about what the Level One containment means?

Oliver Medvedik: So, Level One containment basically means that we work with organisms that are harmless or non-pathogenic. So, essentially, all of the microbes we work with here, all of the organisms, you essentially could work in a high school biology class. So, that’s essentially what BSL1 means technically.

Timothy Lord: Is that from the CDC?

Oliver Medvedik: That is guidelines that were enacted by CDC and the NIH and these are guidelines that are in place throughout the nation and also pretty much throughout the world.

Timothy Lord: So, you are officially certified as well actually physically having those standards?

Oliver Medvedik: So, there’s no official certification process. So, these are guidelines. So, since we don’t deal with any pathogenic organisms, everything here by definition is harmless.

Timothy Lord: Can you show us some of the interesting equipment around?

Oliver Medvedik: Sure. Why don’t you follow me? So, here in this space we have a number of useful items for biotech, over here we have a polymerase chain-reaction machine, so this machine here makes copies of DNA. So, this is a very important piece of gear for any modern molecular biology laboratory. So, you are going to essentially start with one piece of DNA and make millions and millions of copies within an hour. So, before you can actually work with DNA, you need to have sufficient quantities of it and this is one of the key pieces of gear that allows laboratories to work with DNA. So, whether for analysis purposes or to actually take that DNA and manipulate it with regards to genetic engineering, you need to have that raw material to work with and this is one of the key pieces of gear. So, we have two PCR machines here.

Oliver Medvedik: Pretty easy to find on eBay. So, there is certainly a lot of material that you can purchase rather inexpensively, lot of used second-hand equipment. But, again, it’s kind of hard to work with this stuff in your bedroom, because you kind of need a suite of all the other tools that a laboratory has and that’s one of the reasons we started the community biotech lab is for everybody to have shared tools to use in a space like this.

Timothy Lord: And you have been [running] it for three years now?

Oliver Medvedik: So we have been incorporated for the past three years. But, this space that you’re standing in right now, we’ve officially opened our doors to the public in December of 2010, so we’re actually rapidly approaching our second year anniversary.

Timothy Lord: Besides the PCR machine, what else would somebody use that they’re not going to have from the science kit through the mail?

Oliver Medvedik: Right. So we just started doing some protein work, so these are acrylamide gels for doing polyacrylamide gel electrophoresis. So, that term basically, that kind of mouthful of a term, means that you separate proteins. So, we don’t only work with DNA, but we also work with proteins. So, proteins are sort of the business end of DNA. They are the nanomachines of the cell. So, we use these types of apparati to essentially look at proteins.

So, we do protein work here, we have power supplies, so this is a power supply that allows us to separate out molecules, both DNA and proteins. So you need to basically give a strong current, so you can resolve these molecules and then look at them. We have gear here for putting genes into cells, so this is an electroporator. This machine essentially zaps microbes and cells and gets DNA to go inside.

What else do we have? We have a makeshift incubator here for growing plants, so this is actually cobbled together from some leftover restaurant gear, so we have some florescent lights here for growing plants. So, we have a centrifuge here. This is a machine – let me just open this – for spinning samples quite rapidly. So, we have ones that go much faster. This one has a top range of 4,300 RPM. We have ones that go up to 13,000 RPM.

So, this is essentially used for spinning these tubes and when you spin them in a high velocity, things that are more dense collect on the bottom. So, this allows you to separate things based on density. So, that’s a typical piece of gear you find in the laboratory.

Here we have a spectrophotometer. This is a machine that basically shines a beam of light through this little glass or plastic container called a cuvette and this allows you to determine concentrations of things. So basically when a solution changes color, this gives a quantity and tells you how much of that color changes happen. So, you can do various assays. Basically, you can determine if a gene has to be turned on or not turned on. So you need some sort of way to quantitate that, so we use the spectrophotometer for that.

So those are just some of the key items here. We have a dissecting microscope for looking at samples. We have more microscopes in the room behind you.

Timothy Lord: That will be the Hail Mary corner?

Oliver Medvedik: Oh, that’s an inside joke. Ellen actually put that there. We recently were part of a competition called the International Genetically-Engineered Machines competition. It’s an undergrad competition. Right now it’s expanded to about 160 teams around the world. We sponsored the NYU Gallatin team from New York University and we had students from a number of other universities participating here in Genspace using the facilities. So we had students from NYU, we had students from Cooper Union, we even had high school students from Brooklyn Technical High School and a number of other universities.

Our project was essentially to attempt to modify a bacteria that produces cellulose. So, the same type of material you find in paper, so this is actually a sample of bacterial cellulose, right here. So, it kind of looks like parchment. And this bacteria is found in kombucha. It’s essentially the drink that some people like to drink and these sheets basically form and these sheets are the same type of material you find in trees and plants, only bacteria can produce it.

We were trying to and we still are attempting to genetically modify this bacteria to produce other types of biopolymers. And what I mean by biopolymer is a naturally occurring polymer, so unlike polyethylene, cellulose is repeating units of glucose.

There’s also chitin, which is another prevalent biopolymer and that’s found in fungi and insect exoskeleton. So that tough wall you find in insects is a polymer of N-acetylglucosamine unlike cellulose which is polymers of glucose. So, we wanted to see if we can get this bacteria to produce other composite biopolymers.

So, that was our project and this Hail Mary corner, that’s kind of a longwinded answer, but we were doing some last minute work and we got some last minute data, and six hours before we were going to put it on a Web page, and this is where it happened.